# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 20:59:56 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 8-(1,3-benzodioxol-5-ylmethyl)-9-butyl-2-fluoro-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCn1c(Cc2ccc3OCOc3c2)nc4c(N)nc(F)nc14
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 PUX  PUX  8-(1,3-benzodioxol-5-ylmethyl)-9-butyl-2-fluoro-9H-purin-6-amine  ligand  43  25  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PUX
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 PUX  C18   C  CH3   0  -0.662   5.2748   0.0842   1.1019
 PUX  C17   C  CH2   0  -0.428   3.9639  -0.4547   0.5485
 PUX  C16   C  CH2   0  -0.427   2.7475   0.2468   1.1391
 PUX  C15   C  CH2   0  -0.319   1.4519  -0.3336   0.5915
 PUX  N2    N  NR5   0  -0.523   0.2742   0.3491   1.0925
 PUX  C12   C  CR56  0   0.488  -0.3317   0.1120   2.2834
 PUX  N4    N  N     0  -0.491  -0.0182  -0.8095   3.1990
 PUX  C14   C  CR6   0   0.563  -0.8272  -0.7309   4.2181
 PUX  N3    N  N     0  -0.504  -1.8383   0.0692   4.4616
 PUX  C11   C  CR56  0  -0.007  -1.3613   1.0340   2.3687
 PUX  C13   C  CR6   0   0.460  -2.1459   0.9895   3.5357
 PUX  N5    N  NH2   0  -0.810  -3.1687   1.8105   3.7541
 PUX  N1    N  N     0  -0.461  -1.3867   1.8295   1.2544
 PUX  C10   C  CR5   0   0.457  -0.3988   1.4021   0.5180
 PUX  C9    C  CH2   0  -0.601  -0.0273   1.9623  -0.8105
 PUX  C1    C  CR6   0   0.072  -0.2456   1.0048  -1.9618
 PUX  C6    C  CR16  0  -0.398   0.7126   0.9383  -2.9852
 PUX  C5    C  CR56  0   0.312   0.4711   0.0716  -4.0217
 PUX  C2    C  CR16  0  -0.289  -1.3857   0.2147  -2.0218
 PUX  O3    O  O     0  -0.486   1.2263  -0.1584  -5.1220
 PUX  C3    C  CR16  0  -0.327  -1.6188  -0.6669  -3.0839
 PUX  C4    C  CR56  0   0.287  -0.6672  -0.7158  -4.0715
 PUX  O1    O  O     0  -0.486  -0.6517  -1.4588  -5.2057
 PUX  C7    C  CH2   0   0.070   0.6286  -1.2625  -5.7907
 PUX  F     F  F     0  -0.289  -0.5907  -1.6141   5.1877
 PUX  H181  H  HCH3  0   0.230   6.1311  -0.4238   0.6578
 PUX  H182  H  HCH3  0   0.220   5.3804   1.1512   0.8989
 PUX  H183  H  HCH3  0   0.220   5.3328  -0.0523   2.1832
 PUX  H171  H  HCH2  0   0.220   3.9519  -0.3442  -0.5401
 PUX  H172  H  HCH2  0   0.223   3.8952  -1.5286   0.7455
 PUX  H161  H  HCH2  0   0.235   2.7569   0.1529   2.2289
 PUX  H162  H  HCH2  0   0.230   2.7943   1.3172   0.9158
 PUX  H151  H  HCH2  0   0.269   1.4356  -0.2808  -0.4967
 PUX  H152  H  HCH2  0   0.272   1.3619  -1.3880   0.8548
 PUX  H5N1  H  HNH2  0   0.409  -3.6772   1.7767   4.6209
 PUX  H5N2  H  HNH2  0   0.416  -3.4061   2.5267   3.0901
 PUX  H9C1  H  HCH2  0   0.296  -0.6266   2.8636  -0.9540
 PUX  H9C2  H  HCH2  0   0.279   1.0159   2.2897  -0.7985
 PUX  H6    H  HCR6  0   0.274   1.6063   1.5492  -2.9586
 PUX  H2    H  HCR6  0   0.256  -2.1202   0.2748  -1.2283
 PUX  H3    H  HCR6  0   0.274  -2.5108  -1.2776  -3.1194
 PUX  H7C1  H  HCH2  0   0.234   1.2436  -2.1578  -5.6505
 PUX  H7C2  H  HCH2  0   0.246   0.5199  -1.0365  -6.8514

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 PUX  C18  C17   single    1.522  0.020  1.522
 PUX  C18  H181  single    0.970  0.020  1.090
 PUX  C18  H182  single    0.970  0.020  1.090
 PUX  C18  H183  single    0.970  0.020  1.090
 PUX  C17  C16   single    1.523  0.020  1.523
 PUX  C17  H171  single    0.970  0.020  1.090
 PUX  C17  H172  single    0.970  0.020  1.090
 PUX  C16  C15   single    1.522  0.020  1.522
 PUX  C16  H161  single    0.970  0.020  1.090
 PUX  C16  H162  single    0.970  0.020  1.090
 PUX  C15  N2    single    1.451  0.020  1.451
 PUX  C15  H151  single    0.970  0.020  1.090
 PUX  C15  H152  single    0.970  0.020  1.090
 PUX  N2   C12   aromatic  1.357  0.020  1.357
 PUX  N2   C10   aromatic  1.375  0.020  1.375
 PUX  C12  N4    aromatic  1.336  0.020  1.336
 PUX  C12  C11   aromatic  1.385  0.020  1.385
 PUX  N4   C14   aromatic  1.304  0.020  1.304
 PUX  C14  N3    aromatic  1.312  0.020  1.312
 PUX  C14  F     single    1.333  0.020  1.333
 PUX  N3   C13   aromatic  1.341  0.020  1.341
 PUX  C11  C13   aromatic  1.407  0.020  1.407
 PUX  C11  N1    aromatic  1.369  0.020  1.369
 PUX  C13  N5    single    1.330  0.020  1.330
 PUX  N5   H5N1  single    0.860  0.020  1.020
 PUX  N5   H5N2  single    0.860  0.020  1.020
 PUX  N1   C10   aromatic  1.304  0.020  1.304
 PUX  C10  C9    single    1.489  0.020  1.489
 PUX  C9   C1    single    1.513  0.020  1.513
 PUX  C9   H9C1  single    0.970  0.020  1.090
 PUX  C9   H9C2  single    0.970  0.020  1.090
 PUX  C1   C6    aromatic  1.404  0.020  1.404
 PUX  C1   C2    aromatic  1.388  0.020  1.388
 PUX  C6   C5    aromatic  1.372  0.020  1.372
 PUX  C6   H6    single    0.930  0.020  1.080
 PUX  C5   O3    single    1.354  0.020  1.354
 PUX  C5   C4    aromatic  1.385  0.020  1.385
 PUX  C2   C3    aromatic  1.400  0.020  1.400
 PUX  C2   H2    single    0.930  0.020  1.080
 PUX  O3   C7    single    1.423  0.020  1.423
 PUX  C3   C4    aromatic  1.372  0.020  1.372
 PUX  C3   H3    single    0.930  0.020  1.080
 PUX  C4   O1    single    1.356  0.020  1.356
 PUX  O1   C7    single    1.421  0.020  1.421
 PUX  C7   H7C1  single    0.970  0.020  1.090
 PUX  C7   H7C2  single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 PUX  H183  C18  H182  107.55  3.000
 PUX  H183  C18  H181  107.68  3.000
 PUX  H182  C18  H181  107.69  3.000
 PUX  H183  C18  C17   111.21  3.000
 PUX  H182  C18  C17   111.22  3.000
 PUX  H181  C18  C17   111.31  3.000
 PUX  H172  C17  H171  106.12  3.000
 PUX  H172  C17  C16   109.40  3.000
 PUX  H171  C17  C16   109.30  3.000
 PUX  H172  C17  C18   109.65  3.000
 PUX  H171  C17  C18   109.60  3.000
 PUX  C16   C17  C18   112.57  3.000
 PUX  H162  C16  H161  106.67  3.000
 PUX  H162  C16  C15   109.63  3.000
 PUX  H161  C16  C15   109.46  3.000
 PUX  H162  C16  C17   109.71  3.000
 PUX  H161  C16  C17   109.87  3.000
 PUX  C15   C16  C17   111.39  3.000
 PUX  H152  C15  H151  106.66  3.000
 PUX  H152  C15  N2    107.74  3.000
 PUX  H151  C15  N2    108.06  3.000
 PUX  H152  C15  C16   110.62  3.000
 PUX  H151  C15  C16   110.71  3.000
 PUX  N2    C15  C16   112.80  3.000
 PUX  C10   N2   C12   106.37  3.000
 PUX  C10   N2   C15   127.83  3.000
 PUX  C12   N2   C15   125.69  3.000
 PUX  C11   C12  N4    126.26  3.000
 PUX  C11   C12  N2    105.65  3.000
 PUX  N4    C12  N2    128.10  3.000
 PUX  C14   N4   C12   110.39  3.000
 PUX  F     C14  N3    113.95  3.000
 PUX  F     C14  N4    114.75  3.000
 PUX  N3    C14  N4    131.30  3.000
 PUX  C13   N3   C14   117.84  3.000
 PUX  N1    C11  C13   133.09  3.000
 PUX  N1    C11  C12   110.51  3.000
 PUX  C13   C11  C12   116.40  3.000
 PUX  N5    C13  C11   123.07  3.000
 PUX  N5    C13  N3    119.13  3.000
 PUX  C11   C13  N3    117.80  3.000
 PUX  H5N2  N5   H5N1  118.30  3.000
 PUX  H5N2  N5   C13   120.88  3.000
 PUX  H5N1  N5   C13   120.65  3.000
 PUX  C10   N1   C11   104.78  3.000
 PUX  C9    C10  N1    124.72  3.000
 PUX  C9    C10  N2    122.59  3.000
 PUX  N1    C10  N2    112.69  3.000
 PUX  H9C2  C9   H9C1  106.14  3.000
 PUX  H9C2  C9   C1    109.60  3.000
 PUX  H9C1  C9   C1    110.07  3.000
 PUX  H9C2  C9   C10   109.94  3.000
 PUX  H9C1  C9   C10   106.92  3.000
 PUX  C1    C9   C10   113.87  3.000
 PUX  C2    C1   C6    120.14  3.000
 PUX  C2    C1   C9    120.76  3.000
 PUX  C6    C1   C9    119.09  3.000
 PUX  H6    C6   C5    121.34  3.000
 PUX  H6    C6   C1    121.25  3.000
 PUX  C5    C6   C1    117.41  3.000
 PUX  C4    C5   O3    109.43  3.000
 PUX  C4    C5   C6    122.06  3.000
 PUX  O3    C5   C6    128.51  3.000
 PUX  H2    C2   C3    118.55  3.000
 PUX  H2    C2   C1    119.59  3.000
 PUX  C3    C2   C1    121.86  3.000
 PUX  C7    O3   C5    106.22  3.000
 PUX  H3    C3   C4    121.88  3.000
 PUX  H3    C3   C2    121.18  3.000
 PUX  C4    C3   C2    116.94  3.000
 PUX  O1    C4   C3    129.01  3.000
 PUX  O1    C4   C5    109.40  3.000
 PUX  C3    C4   C5    121.59  3.000
 PUX  C7    O1   C4    106.20  3.000
 PUX  H7C2  C7   H7C1  110.50  3.000
 PUX  H7C2  C7   O1    109.84  3.000
 PUX  H7C1  C7   O1    109.89  3.000
 PUX  H7C2  C7   O3    109.78  3.000
 PUX  H7C1  C7   O3    109.78  3.000
 PUX  O1    C7   O3    106.99  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 PUX  CONST_01  C14   N4   C12  N2    180.00   0.0  0
 PUX  CONST_02  C13   C11  C12  N2    180.00   0.0  0
 PUX  CONST_03  N1    C11  C12  N2      0.00   0.0  0
 PUX  CONST_04  C11   N1   C10  N2      0.00   0.0  0
 PUX  CONST_05  N1    C10  N2   C12     0.00   0.0  0
 PUX  CONST_06  N3    C14  N4   C12     0.00   0.0  0
 PUX  CONST_07  N3    C13  C11  C12     0.00   0.0  0
 PUX  CONST_08  C10   N1   C11  C12     0.00   0.0  0
 PUX  CONST_09  C10   N2   C12  N4    180.00   0.0  0
 PUX  CONST_10  C13   C11  C12  N4      0.00   0.0  0
 PUX  CONST_11  N1    C11  C12  N4    180.00   0.0  0
 PUX  CONST_12  C13   N3   C14  N4      0.00   0.0  0
 PUX  CONST_13  C11   C12  N4   C14     0.00   0.0  0
 PUX  CONST_14  C11   C13  N3   C14     0.00   0.0  0
 PUX  CONST_15  N1    C11  C13  N3    180.00   0.0  0
 PUX  CONST_16  C10   N2   C12  C11     0.00   0.0  0
 PUX  CONST_17  C10   N1   C11  C13   180.00   0.0  0
 PUX  CONST_18  C4    C5   C6   C1      0.00   0.0  0
 PUX  CONST_19  C4    C3   C2   C1      0.00   0.0  0
 PUX  CONST_20  C3    C2   C1   C6      0.00   0.0  0
 PUX  CONST_21  C3    C4   C5   C6      0.00   0.0  0
 PUX  CONST_22  C2    C1   C6   C5      0.00   0.0  0
 PUX  CONST_23  C2    C3   C4   C5      0.00   0.0  0
 PUX  CONST_24  N4    C12  N2   C15     0.00   0.0  0
 PUX  CONST_25  C11   C12  N2   C15   180.00   0.0  0
 PUX  CONST_26  N1    C10  N2   C15   180.00   0.0  0
 PUX  CONST_27  C9    C10  N2   C12   180.00   0.0  0
 PUX  CONST_28  F     C14  N4   C12   180.00   0.0  0
 PUX  CONST_29  N5    C13  C11  C12   180.00   0.0  0
 PUX  CONST_30  N5    C13  N3   C14   180.00   0.0  0
 PUX  CONST_31  C9    C10  N1   C11   180.00   0.0  0
 PUX  CONST_32  F     C14  N3   C13   180.00   0.0  0
 PUX  CONST_33  N1    C11  C13  N5      0.00   0.0  0
 PUX  CONST_34  C5    C6   C1   C9    180.00   0.0  0
 PUX  CONST_35  C3    C2   C1   C9    180.00   0.0  0
 PUX  CONST_36  H3    C3   C2   C1    180.00   0.0  0
 PUX  CONST_37  H2    C2   C1   C6    180.00   0.0  0
 PUX  CONST_38  H6    C6   C1   C2    180.00   0.0  0
 PUX  CONST_39  H5N1  N5   C13  N3      0.00   0.0  0
 PUX  CONST_40  H5N2  N5   C13  N3    180.00   0.0  0
 PUX  Var_01    O1    C7   O3   C5     12.92  30.0  1
 PUX  Var_02    C1    C9   C10  N2     65.95  30.0  2
 PUX  Var_03    C6    C1   C9   C10  -139.36  30.0  2
 PUX  Var_04    C12   N2   C15  C16   -82.70  30.0  2
 PUX  Var_05    N2    C15  C16  C17  -177.63  30.0  3
 PUX  Var_06    C15   C16  C17  C18  -178.71  30.0  3
 PUX  Var_07    H181  C18  C17  C16  -179.36  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 PUX  plan-1  C15   0.020
 PUX  plan-1  N2    0.020
 PUX  plan-1  C12   0.020
 PUX  plan-1  N4    0.020
 PUX  plan-1  C14   0.020
 PUX  plan-1  N3    0.020
 PUX  plan-1  C11   0.020
 PUX  plan-1  C13   0.020
 PUX  plan-1  N5    0.020
 PUX  plan-1  N1    0.020
 PUX  plan-1  C10   0.020
 PUX  plan-1  C9    0.020
 PUX  plan-1  F     0.020
 PUX  plan-2  C9    0.020
 PUX  plan-2  C1    0.020
 PUX  plan-2  C6    0.020
 PUX  plan-2  C5    0.020
 PUX  plan-2  C2    0.020
 PUX  plan-2  O3    0.020
 PUX  plan-2  C3    0.020
 PUX  plan-2  C4    0.020
 PUX  plan-2  O1    0.020
 PUX  plan-2  H6    0.020
 PUX  plan-2  H2    0.020
 PUX  plan-2  H3    0.020
 PUX  plan-3  C13   0.020
 PUX  plan-3  N5    0.020
 PUX  plan-3  H5N1  0.020
 PUX  plan-3  H5N2  0.020

